rs144936173
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000722.4(CACNA2D1):c.831C>T(p.Ser277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,609,368 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S277S) has been classified as Likely benign.
Frequency
Consequence
NM_000722.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA2D1 | NM_000722.4 | c.831C>T | p.Ser277= | synonymous_variant | 10/39 | ENST00000356860.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA2D1 | ENST00000356860.8 | c.831C>T | p.Ser277= | synonymous_variant | 10/39 | 1 | NM_000722.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000466 AC: 7AN: 150108Hom.: 1 Cov.: 29
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250638Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135448
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1459260Hom.: 0 Cov.: 29 AF XY: 0.0000427 AC XY: 31AN XY: 726084
GnomAD4 genome ? AF: 0.0000466 AC: 7AN: 150108Hom.: 1 Cov.: 29 AF XY: 0.0000547 AC XY: 4AN XY: 73116
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Brugada syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2023 | - - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at